public:
- ListSeqsCommand(string);
- ~ListSeqsCommand(){};
- int execute();
- void help();
-
+ ListSeqsCommand(string);
+ ListSeqsCommand();
+ ~ListSeqsCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "get.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
+
private:
- vector<string> names;
- string fastafile, namefile, groupfile, alignfile, inputFileName;
+ vector<string> names, outputNames;
+ string fastafile, namefile, groupfile, alignfile, inputFileName, outputDir, listfile, taxfile;
bool abort;
- void readFasta();
- void readName();
- void readGroup();
- void readAlign();
+ int readFasta();
+ int readName();
+ int readGroup();
+ int readAlign();
+ int readList();
+ int readTax();
};